BioPerl Remote Blast with Gene ID only ?

Question

[ksi216]

I'm new to BioPerl. I've been reading the howtos and looked at sample scripts, but it doesn't seem that I can run a blast using gene Ids only? I've been looking and it doesn't really mention that. I just wanted to know if it can be done and a sample syntax?

Answer 1

[SES]

BLAST is a sequence comparison tool, so no, you can't pass only an ID. You'll need to pull out the sequence first and then pass it to the RemoteBlast module. You can fetch a list of sequences from Genbank (check out the efetch HOWTOs) with bioperl and then run the BLAST search. That would be my suggestion based on what you have provided.

[ksi216]

is there any website that I can input Gene Id's and it will give me Fasta sequences ?

[SES]

Sorry, I missed your comment. Of course you can search by ID but the place you'll want to search depends on the ID source (e.g., Uniprot or Genbank). Once you get a list, you can do that with a BioPerl as I mentioned.